BN0934 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 2.4322e-05 3.9260e-04
Layer 6 5.1697e-05 1.1734e-03
Layer 3 5.4968e-05 6.6017e-03
Layer 5 7.8156e-04 3.3093e-03
Layer 2 3.9812e-03 1.1498e-01
WM 9.8708e-01 5.2413e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.3086 0.7225
SH3GL2 Layer 6 2.4297 0.6535
GOT1 Layer 6 2.1914 0.6435
STMN2 Layer 5 2.1152 0.6408
CHGA Layer 4 2.5176 0.6365
PFKP Layer 5 2.3438 0.6321
NAPB Layer 6 2.2266 0.6281
SPOCK1 Layer 6 2.4180 0.6241
NDRG4 Layer 4 2.2617 0.6202
SYT4 Layer 6 2.5332 0.6131
SEZ6L2 Layer 4 2.2676 0.6108
KIF1A Layer 6 2.1445 0.6087
TUBB Layer 6 2.0488 0.6077
SULT4A1 Layer 4 2.1621 0.6054
PRDX1 Layer 4 2.1387 0.6030
ATP6V0B Layer 6 2.1152 0.6029
SYNGR3 Layer 5 2.2832 0.6016
SYP Layer 5 2.0820 0.5991
CPLX1 Layer 4 2.3340 0.5978
MORF4L1 Layer 4 2.1875 0.5966
FKBP8 Layer 6 2.2266 0.5962
SV2B Layer 6 2.3086 0.5957
REEP5 Layer 4 2.1621 0.5910
TTC9B Layer 4 2.3711 0.5892
SV2A Layer 4 2.3594 0.5892
FBXW7 Layer 6 2.3711 0.5886
CADPS2 Layer 4 2.0957 0.5876
TAGLN3 Layer 4 2.2422 0.5869
NDUFB8 Layer 6 2.1016 0.5847
BMERB1 Layer 4 2.2266 0.5845
PFN2 Layer 4 2.2266 0.5844
CAMK2G Layer 4 2.2773 0.5841
PCLO Layer 4 2.2715 0.5828
ATP6V1A Layer 6 2.2578 0.5809
EFHD2 Layer 6 2.5000 0.5809
ENO2 Layer 4 2.1543 0.5806
STMN1 Layer 4 1.9141 0.5806
LMO4 Layer 6 2.2461 0.5797
IQSEC1 Layer 4 2.4336 0.5795
APBB1 Layer 6 2.2168 0.5783
EEF1A2 Layer 6 2.1289 0.5780
SPOCK2 Layer 4 2.2168 0.5780
STX1A Layer 6 2.3281 0.5778
SOD1 Layer 5 2.0352 0.5764
STX1B Layer 4 2.1094 0.5764
SYN2 Layer 4 2.2227 0.5758
SLC17A7 Layer 6 2.0859 0.5756
KLHDC3 Layer 6 2.2324 0.5753
CAMK2B Layer 6 2.3398 0.5747
NDFIP1 Layer 6 2.1445 0.5747

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0934
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0934_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0934/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0934/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0934/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0934/report/PD/BN0934_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0934/report/PD/BN0934_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 01:51:03
  • Number of Processes: 10
  • Spending Time: 0h 3m